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Novel GH12 endogluconase from Aspergillus cervinus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 288 Peg 6000 18,5%
0.2M CaCl2
0.1M NaAcetate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.094 α = 90 b = 118.364 β = 90 c = 125.702 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.17 125.7 99.6 0.152 0.18 0.095 0.995 7.8 6.5 37115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.24 0.715 0.862 0.475 0.866 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5GM3 2.17 62.93 37069 1893 99.389 0.186 0.1835 0.1835 0.2305 0.2305 30.421
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 7.06 -3.219 -3.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.605 r_dihedral_angle_4_deg 28.415 r_dihedral_angle_3_deg 11.755 r_dihedral_angle_1_deg 7.511 r_lrange_it 5.785 r_scangle_it 3.921 r_mcangle_it 3.48 r_scbond_it 3.175 r_mcbond_it 2.471 r_angle_refined_deg 1.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.605 r_dihedral_angle_4_deg 28.415 r_dihedral_angle_3_deg 11.755 r_dihedral_angle_1_deg 7.511 r_lrange_it 5.785 r_scangle_it 3.921 r_mcangle_it 3.48 r_scbond_it 3.175 r_mcbond_it 2.471 r_angle_refined_deg 1.413 r_metal_ion_refined 0.53 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.286 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 r_ncsr_local_group_1 0.074 r_ncsr_local_group_2 0.07 r_ncsr_local_group_3 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5120 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing